KLinPopup is a program like Linpopup,
Linpopup2 (Gtk2+) or
KPopup (heavily based on this)
to receive and send Windows popup messages (Winpopup or "net send") with Unix/Linux.
It uses Samba to do this. You should be able to receive/send messages from/to OSs where Samba is running on (e.g. BSDs, Linux, OSX) and of course Windows 2000/XP. For Windows 95/ME you need an additional Winpopup program.

Also Kopete can handle winpopup messages (works in 0.12 again).
Kopete 0.12beta2 is out, packages for various distributions are here.